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Controlling biocatalytic cascades with enzyme–DNA dynamic networks

Nature Catalysis volume 3, pages 941–950 (2020)Cite this article

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Abstract

Cellular transformations, such as gene expression or temporal protein activities, are controlled by complex stimuli-responsive network circuitries regulated by enzymes, metabolites or transcription factors. Inspired by nature, extensive research efforts are directed to mimic these processes by in vitro chemical systems. Here we report on the assembly of constitutional dynamic networks (CDNs), composed of nucleic acid–enzyme conjugates, that act as modules for triggered, network-driven, biocatalytic cascades and for the intercommunication of network-guided biocatalytic cascades. Two CDNs were assembled—one network includes a constituent module functionalized with glucose oxidase and horseradish peroxidase in spatially close positions, and the second CDN includes a constituent module modified at sterically intimate positions with nicotinamide adenine dinucleotide and alcohol dehydrogenase. Biocatalytic cascades proceed in the two networks and, on the triggered reconfiguration of the CDNs, controlled and switchable biocatalytic cascades in the CDNs are demonstrated. The two CDNs are coupled, and the triggered feedback-driven intercommunication of the networks is realized.

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Fig. 1: Reversible triggered reconfiguration of a network-driven bienzyme cascade.
Fig. 2: Reversible triggered reconfiguration of a network-driven enzyme/cofactor cascade.
Fig. 3: Orthogonal operation of two biocatalytic cascades guided by intercommunicating dynamic networks.
Fig. 4: Feedback-driven intercommunication of networks M and N that activate two coupled biocatalytic cascades.

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Data availability

The data that support the plots within this paper and other findings of this study are available from the corresponding authors upon reasonable request. Source data are provided with this paper.

References

  1. Fell, D. A. & Wagner, A. The small world of metabolism. Nat. Biotechnol. 18, 1121–1122 (2000).

    CAS  PubMed  Google Scholar 

  2. Guelzim, N., Bottani, S., Bourgine, P. & Képès, F. Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet. 31, 60–63 (2002).

    CAS  PubMed  Google Scholar 

  3. Davidson, E. H. et al. A genomic regulatory network for development. Science 295, 1669–1678 (2002).

    CAS  PubMed  Google Scholar 

  4. Barabási, A. L. & Oltvai, Z. N. Network biology: understanding the cell’s functional organization. Nat. Rev. Genet. 5, 101–113 (2004).

    PubMed  Google Scholar 

  5. Oliveri, P. & Davidson, E. H. Gene regulatory network controlling embryonic specification in the sea urchin. Curr. Opin. Genet. Dev. 14, 351–360 (2004).

    CAS  PubMed  Google Scholar 

  6. Levine, M. & Davidson, E. H. Gene regulatory networks for development. Proc. Natl Acad. Sci. USA 102, 4936–4942 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Peter, I. S. & Davidson, E. H. Assessing regulatory information in developmental gene regulatory networks. Proc. Natl Acad. Sci. USA 114, 5862–5869 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Montagne, K., Plasson, R., Sakai, Y., Fujii, T. & Rondelez, Y. Programming an in vitro DNA oscillator using a molecular networking strategy. Mol. Syst. Biol. 7, 466 (2011).

    PubMed  PubMed Central  Google Scholar 

  9. Weitz, M. et al. Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. Nat. Chem. 6, 295–302 (2014).

    CAS  PubMed  Google Scholar 

  10. Semenov, S. N. et al. Rational design of functional and tunable oscillating enzymatic networks. Nat. Chem. 7, 160–165 (2015).

    CAS  PubMed  Google Scholar 

  11. Schaffter, S. W. & Schulman, R. Building in vitro transcriptional regulatory networks by successively integrating multiple functional circuit modules. Nat. Chem. 11, 829–838 (2019).

    CAS  PubMed  Google Scholar 

  12. Kim, J., White, K. S. & Winfree, E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol. Syst. Biol. 2, 68 (2006).

    PubMed  PubMed Central  Google Scholar 

  13. Wang, F., Liu, X. & Willner, I. DNA switches: from principles to applications. Angew. Chem. Int. Ed. 54, 1098–1129 (2015).

    CAS  Google Scholar 

  14. Lu, C. H. et al. Switchable catalytic acrylamide hydrogels cross-linked by hemin/G-quadruplexes. Nano Lett. 13, 1298–1302 (2013).

    CAS  PubMed  Google Scholar 

  15. Liu, D. & Balasubramanian, S. A proton-fuelled DNA nanomachine. Angew. Chem. Int. Ed. 42, 5734–5736 (2003).

    CAS  Google Scholar 

  16. Hu, Y., Cecconello, A., Idili, A., Ricci, F. & Willner, I. Triplex DNA nanostructures: from basic properties to applications. Angew. Chem. Int. Ed. 56, 15210–15233 (2017).

    CAS  Google Scholar 

  17. Liang, X., Mochizuki, T. & Asanuma, H. A supra-photoswitch involving sandwiched DNA base pairs and azobenzenes for light-driven nanostructures and nanodevices. Small 5, 1761–1768 (2009).

    CAS  PubMed  Google Scholar 

  18. Asanuma, H. et al. Enantioselective incorporation of azobenzenes into oligodeoxyribonucleotide for effective photoregulation of duplex formation. Angew. Chem. Int. Ed. 40, 2671–2673 (2001).

    CAS  Google Scholar 

  19. Zhang, D. Y. & Seelig, G. Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3, 103–113 (2011).

    CAS  PubMed  Google Scholar 

  20. Seeman, N. C. DNA in a material world. Nature 421, 427–431 (2003).

    PubMed  Google Scholar 

  21. Lu, C. H., Willner, B. & Willner, I. DNA nanotechnology: from sensing and DNA machines to drug-delivery systems. ACS Nano 7, 8320–8332 (2013).

    CAS  PubMed  Google Scholar 

  22. Teller, C. & Willner, I. Functional nucleic acid nanostructures and DNA machines. Curr. Opin. Biotechnol. 21, 376–391 (2010).

    CAS  PubMed  Google Scholar 

  23. Bath, J. & Turberfield, A. J. DNA nanomachines. Nat. Nanotechnol. 2, 275–284 (2007).

    CAS  PubMed  Google Scholar 

  24. Seeman, N. C. From genes to machines: DNA nanomechanical devices. Trends Biochem. Sci. 30, 119–125 (2012).

    Google Scholar 

  25. Wang, S. et al. Controlling the catalytic functions of DNAzymes within constitutional dynamic networks of DNA nanostructures. J. Am. Chem. Soc. 139, 9662–9671 (2017).

    CAS  PubMed  Google Scholar 

  26. Wang, S. et al. Light-induced reversible reconfiguration of DNA-based constitutional dynamic networks: application to switchable catalysis. Angew. Chem. Int. Ed. 57, 8105–8109 (2018).

    CAS  Google Scholar 

  27. Yue, L., Wang, S. & Willner, I. Triggered reversible substitution of adaptive constitutional dynamic networks dictates programmed catalytic functions. Sci. Adv. 5, eaav5564 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Zhou, Z., Yue, L., Wang, S., Lehn, J. M. & Willner, I. DNA-based multiconstituent dynamic networks: hierarchical adaptive control over the composition and cooperative catalytic functions of the systems. J. Am. Chem. Soc. 140, 12077–12089 (2018).

    CAS  PubMed  Google Scholar 

  29. Yue, L. et al. Consecutive feedback-driven constitutional dynamic networks. Proc. Natl Acad. Sci. USA 116, 2843–2848 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Yue, L. et al. Intercommunication of DNA-based constitutional dynamic networks. J. Am. Chem. Soc. 140, 8721–8731 (2018).

    CAS  PubMed  Google Scholar 

  31. Yue, L., Wang, S. & Willner, I. Three-dimensional nucleic-acid-based constitutional dynamic networks: enhancing diversity through complexity of the systems. J. Am. Chem. Soc. 141, 16461–16470 (2019).

    CAS  PubMed  Google Scholar 

  32. Jitrapakdee, S. et al. Structure, mechanism and regulation of pyruvate carboxylase. Biochem. J. 413, 369–387 (2008).

    CAS  PubMed  Google Scholar 

  33. Vázquez-González, M., Wang, C. & Willner, I. Biocatalytic cascades operating on macromolecular scaffolds and in confined environments. Nat. Catal. 3, 256–273 (2020).

    Google Scholar 

  34. Elani, Y., Law, R. V. & Ces, O. Vesicle-based artificial cells as chemical microreactors with spatially segregated reaction pathways. Nat. Commun. 5, 5305 (2014).

    CAS  PubMed  Google Scholar 

  35. Vriezema, D. M. et al. Positional assembly of enzymes in polymersome nanoreactors for cascade reactions. Angew. Chem. Int. Ed. 46, 7378–7382 (2007).

    CAS  Google Scholar 

  36. Liang, J. et al. Peptide-induced super-assembly of biocatalytic metal–organic frameworks for programmed enzyme cascades. Chem. Sci. 10, 7852–7858 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Chen, W. H., Vázquez-González, M., Zoabi, A., Abu-Reziq, R. & Willner, I. Biocatalytic cascades driven by enzymes encapsulated in metal–organic framework nanoparticles. Nat. Catal. 1, 689–695 (2018).

    CAS  Google Scholar 

  38. Wilner, O. I. et al. Enzyme cascades activated on topologically programmed DNA scaffolds. Nat. Nanotechnol. 4, 249–254 (2009).

    CAS  PubMed  Google Scholar 

  39. Fu, J. et al. Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm. Nat. Nanotechnol. 9, 531–536 (2014).

    CAS  PubMed  Google Scholar 

  40. Ngo, T. A., Nakata, E., Saimura, M. & Morii, T. Spatially organized enzymes drive cofactor-coupled cascade reactions. J. Am. Chem. Soc. 138, 3012–3021 (2016).

    CAS  PubMed  Google Scholar 

  41. Xin, L., Zhou, C., Yang, Z. & Liu, D. Regulation of an enzyme cascade reaction by a DNA machine. Small 9, 3088–3091 (2013).

    CAS  PubMed  Google Scholar 

  42. Yang, Y. et al. Programming rotary motions with a hexagonal DNA nanomachine. Chem. Eur. J. 25, 5158–5162 (2019).

    CAS  PubMed  Google Scholar 

  43. Qu, J. et al. Synthetic multienzyme complexes, catalytic nanomachineries for cascade biosynthesis in vivo. ACS Nano 13, 9895–9906 (2019).

    CAS  PubMed  Google Scholar 

  44. You, C., Myung, S. & Zhang, Y. H. P. Facilitated substrate channeling in a self-assembled trifunctional enzyme complex. Angew. Chem. Int. Ed. 51, 8787–8790 (2012).

    CAS  Google Scholar 

  45. Lin, J. L., Palomec, L. & Wheeldon, I. Design and analysis of enhanced catalysis in scaffolded multienzyme cascade reactions. ACS Catal. 4, 505–511 (2014).

    CAS  Google Scholar 

  46. Zhang, Y. & Hess, H. Toward rational design of high-efficiency enzyme cascades. ACS Catal. 7, 6018–6027 (2017).

    CAS  Google Scholar 

  47. Lancaster, L., Abdallah, W., Banta, S. & Wheeldon, I. Engineering enzyme microenvironments for enhanced biocatalysis. Chem. Soc. Rev. 47, 5177–5186 (2018).

    CAS  PubMed  Google Scholar 

  48. Lin, J. L. & Wheeldon, I. Kinetic enhancements in DNA–enzyme nanostructures mimic the Sabatier principle. ACS Catal. 3, 560–564 (2013).

    CAS  Google Scholar 

  49. Idan, O. & Hess, H. Origins of activity enhancement in enzyme cascades on scaffolds. ACS Nano 7, 8658–8665 (2013).

    CAS  PubMed  Google Scholar 

  50. Ellis, G. A. et al. Artificial multienzyme scaffolds: pursuing in vitro substrate channeling with an overview of current progress. ACS Catal. 9, 10812–10869 (2019).

    CAS  Google Scholar 

  51. Tigges, M., Marquez-Lago, T. T., Stelling, J. & Fussenegger, M. A tunable synthetic mammalian oscillator. Nature 457, 309–312 (2009).

    CAS  PubMed  Google Scholar 

  52. Fung, E. et al. A synthetic gene–metabolic oscillator. Nature 435, 118–122 (2005).

    CAS  PubMed  Google Scholar 

  53. Wu, Q. et al. Cascade enzymes within self-assembled hybrid nanogel mimicked neutrophil lysosomes for singlet oxygen elevated cancer therapy. Nat. Commun. 10, 240 (2019).

    PubMed  PubMed Central  Google Scholar 

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Acknowledgements

Our research is supported by the Israel Science Foundation.

Author information

Authors and Affiliations

  1. Institute of Chemistry, The Minerva Center for Complex Bio-hybrid Systems, The Hebrew University of Jerusalem, Jerusalem, Israel

    Chen Wang, Liang Yue & Itamar Willner

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  1. Chen Wang
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  2. Liang Yue
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  3. Itamar Willner
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Contributions

C.W. performed the experiments, analysed the results and participated in writing the paper. L.Y. participated in the design of CDNs and analysis of the results. I.W. supervised the project.

Corresponding author

Correspondence to Itamar Willner.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

Supplementary Methods, Figs. 1–33, discussion, Tables 1–4, Notes 1–4 and references.

Source data

Source Data Fig. 1

Time-dependent fluorescence changes generated by the DNAzyme reporter units associated with the constituents in CDNs and time-dependent absorbance changes of ABTS∙– in CDNs.

Source Data Fig. 2

Time-dependent fluorescence changes generated by the DNAzyme reporter units associated with the constituents in CDNs and time-dependent absorbance changes induced by ADH/NAD+/MB+ cascade and ADH/NAD+/pyruvic acid cascade.

Source Data Fig. 3

Time-dependent absorbance changes induced by two biocatalytic cascades guided by intercommunicating CDNs.

Source Data Fig. 4

Time-dependent absorbance changes of two biocatalytic cascades guided by feedback-driven intercommunication of coupled CDNs.

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Wang, C., Yue, L. & Willner, I. Controlling biocatalytic cascades with enzyme–DNA dynamic networks. Nat Catal 3, 941–950 (2020). https://doi.org/10.1038/s41929-020-00524-7

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